Pavel P. Kuksa



SparkINFERNO: a scalable high-throughput pipeline for inferring molecular mechanisms of non-coding ge-netic variants Bitbucket repository
HIPPIE2: a method for fine-scale identification of physically interacting chromatin regions Bitbucket repository
HIPR: High-throughput probabilistic inference of RNA structures HIPR website
Alignment-free Analysis and Prediction for DNA Barcode data
Project page (data+code)
String kernels in C
Mismatch, spectrum, gapped, wildcard string kernels
Project page (data+code)
Multi-class protein fold recognition
Project page (data+code)
Spatial kernels in C (SSSK)
Project page (data+code)
Sparse Spatial Kernels for Efficient Large Scale Sequence Classification
Project page (data+code)
High-throughput Annotation of Modified Ribonucleotides
Github project
Multi-variate sequence kernels
Motif finding for large-alphabet inputs



DASHR: Human non-coding RNA database DASHR
DASHR 2.0: integrated database of human small non-coding RNA genes and mature products DASHR2

Web servers

SPAR: small RNA-seq portal for analysis of sequencing experiments SPAR web server
SPAR pipeline bitbucket repository
HAMR: High-throughput Annotation of Modified Ribonucleotides GitHub repository
HAMR website